Forging Ahead
by Acrocera
Summary: The battle for Earth is reaching its climax, and Shepard is nowhere to be found.  An attempt at a realistic sequence of events following Harbinger's attack.
1. Chapter 1

This is my first story; I have been a long-time lurker here and have decided to buckle down and contribute. I, like so many others, take issue with the end of Mass Effect 3 and I choose to accept an indoctrination theory of sorts. Mine is a Paragon FemShep, loyal to Liara, Spacer, War Hero. What can I say, I'm a sucker for the quintessential "good guy". There are elements I have left out of this first chapter purposefully (the Crucible, the Catalyst, etc.) and more clarity will come with later chapters.

If those of you feel the inclination, please let me know what you think. Now, on with the story!

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><p>"Focus your fire on the oculi!" The command from Admiral Hackett blasted through the communications channels. The Reapers had paused, something had happened. The combined forces of organics and Geth were not going to waste this opportunity.<p>

All ships and ground troops opened fire on the immobilized Reapers. The pause was no more than thirty seconds, but in that short time, they were crippled. Reapers were falling across the galaxy. Even those that had survived the onslaught would not survive much longer. The organics had pulled ahead.

After several hours of fighting, Harbinger finally succumbed to fire. The massive Reaper fell dead in the streets of London, the last of its kind. Communications channels were buzzing with reports of conquered Reapers from all over the world and throughout the galaxy.

Victory.

"Garrus!" A frantic voice called out again and again. "Shepard!"

"Normandy, this is Liara, I cannot locate Garrus or the Commander, can you get a read on their position?" Dr. T'Soni was frantic, there was only rubble and smoke for as far as she could see. Some larger structures had survived, but the streets were littered with the remnants of war.

"Negative Doctor. I'm sending more of the crew to your location; sit tight. We'll find them, Liara." Joker tried to be as comforting as possible. He grimaced and finished alerting the other crew members of their new search and rescue mission. "It can't end like this EDI, it just… can't."

"The Commander had 0.000141% of surviving a direct hit from a Reaper. If Dr. T'Soni's report was accurate, then it is unlikely that we will find the Commander at all." EDI hesitated, managing to seem awkward. "However, Shepard has overcome insurmountable odds in the past; perhaps she will pull through Jeff."

"Shit." Was all Joker could say. "We've gotta try, EDI. We owe her that."

"Joker have the rest of the ground team meet me down in the armory." Joker jumped as Ashley came over the intercom.

"You're clear LC Williams. Team is being notified now."

Down in the armory Ashley Williams paced back and forth as she waited for the rest of the crew to assemble. Almost the entire crew had rendezvoused back at the Normandy after Harbinger had fallen. Dr. Chakwas had seen to the more serious injuries, but those that had only minor scrapes and burns were left to help one another. Ashley hastily treated her own scrapes and burns, then moved on to the other crew members. She roughly bandaged one private's leg, unable to concentrate on technique. Williams knew she was racing against the clock; that every moment spent in preparation pushed Shepard closer to death. That is, if she had even survived.

"Um… Ma'am?" James ventured carefully, hesitant to break the Lieutenant Commander's concentration. "We're all here."

Ashley's head snapped up and she surveyed her team. Vega was shifting nervously, his normal bravado having crumbled hours ago. He was relatively uninjured, only a few cuts here and there. Javik stood almost perfectly still, his eyes seemed to bore into Ashley as she looked at him. Tali's helmet had been cracked and there were multiple tears on her suit. She had hastily patched what she could and loaded up on Medi-gel and anti-biotics to combat the impending illness. Her breathing was uneven, but she had refused to stay behind. Wrex had also joined their squad. He was limping; it looked like half of his foot had been blown off. Even EDI seemed to have taken a beating. The dents and scorch marks on her metal exterior indicated that the AI had seen some serious combat of her own.

Williams motioned for the group to pile uncomfortably into the heavily damaged, secondary shuttle. James got behind the controls and started them off toward Liara's location.

"Okay people, listen up." Ashley tried with everything she could muster to sound as confident as Commander Shepard. It was a battle for her to keep her hands from shaking and her voice from wavering. "We are missing two of our team. Garrus and Shepard are out there somewhere. We didn't come this far to lose them like this. We'll split into three teams. Wrex, you and Tali will be with Liara. EDI is with Javik and Vega comes with me. I don't think we will have to worry too much about Reaper ground forces. Once the big guys started falling, the freak show got hammered. But just in case, keep an eye out. Our primary objective is finding the Commander and Garrus. Any other rescue efforts are secondary. We owe it to Shepard to give it everything we've got. You know what she means to all of us, I don't need to spell it out. Get out there and find her. Bring her home."

With that the cabin of the shuttle was silent. Once Vega found a safe landing area close to Liara, the team piled out.

"Thank the Goddess you've arrived! I have been searching but I… I cannot find them." She blinked back tears. She was beyond exhausted and utterly overwhelmed, but she could not, would not stop until she found Shepard. Her shoulder had been dislocated and her right arm was hanging awkwardly at her side.

Tali walked briskly to Liara and pulled her into a gentle hug, avoiding the damaged shoulder. "We're with you Doc." Wrex rumbled as gently as he could. Liara pulled herself together and nodded.

After two hours of searching, the team got a morale boost.

"Lieutenant Commander Williams." EDI called over the channel to Ashley, but was heard by the entire team. "Javik has located Admiral Vakarian. His left arm was pinned under rubble, smashing his omni-tool. He is unconscious, but his vitals appear to be stable. I will radio Joker for pickup."

"You're clear EDI. Good work you two. When you get Garrus secured, get back down here."

Several hours after Garrus had been found, the search for Shepard had proved unsuccessful. Ashley was torn. To leave the Commander out here seemed unthinkable, but she could not imagine that her CO had been able to survive this long. She made up her mind. "Meet me back at the shuttle everyone."

"What?" Liara's voice was panicked. She had grown increasingly frantic as the hours wore on. "You cannot be serious. I will not leave Shepard out here. I must find her."

"We've been through a hell of a day Liara, if we don't get some rest we get sloppy. We can continue searching after we get some sleep. We won't be able to help the Commander if we're walking around like zombies." Ashley heard Liara's scream of protest over the radio. "Everyone goes back to the Normandy tonight. That's an order."

"No. I will continue to search. I will not abandon her!" Liara had reached her emotional limit. Tears of rage streaked down her face. Her head was pounding and her stomach was in upheaval at the thought of abandoning her bondmate.

Ashley shook her head. She hated herself for ordering the team to fall back; but she knew it's what Shepard would have wanted. Shepard would not want her friends coming to harm for her sake. "Bring her in Wrex, however you need to."

With that Wrex grabbed Liara and threw her over his shoulder. "Put me down at once!" She yelled in protest. "You are making a mistake! WREX!" Liara pounded on his back with her good arm until she dissolved into tears, accepting defeat.

The team sat in the Normandy's conference room. They had all been attended to by Chakwas after Garrus had been stabilized. Liara was no longer crying, but sat in a daze, staring at the table top. They had been unable to find Shepard. They all knew there was little use in going back. Shepard could not have survived Harbinger's attack without immediate medical treatment – if it was survivable at all.

"We tried." Was all Ashley could say. Everything seemed hollow. She felt as if her very existence was a mockery. She had let down the woman she respected most.

"Lieutenant Commander!" Joker's voice rang through the ship excitedly.

"What is it Joker?" Ashley sighed. She felt broken.

"I just received a communication from an Alliance ground clinic. They found an N7 Marine. She was alive, but just barely." The team perked up, not daring to even breathe, afraid that the littlest thing would cause disruption. "They think its Shepard."


	2. Chapter 2

Thank you so much for the favorites and follows! I must thank countwes and Pink Starship personally for the encouragement. As always, feedback is very much appreciated by this novice.

On with the story!

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><p>"Shepard, save us. Shepard!" The disembodied voices rang through her thoughts. The forest, that damn forest was all around her. She spotted the boy, the one who had been haunting her through all of this.<p>

"Wait!" Commander Shepard called to him. "Come back!"

She took off running as fast as she could, but she couldn't quite catch him. She never could. Finally, he stopped and turned around. As he turned she could see that his appearance had changed, he was no longer a thing of flesh and blood, but made entirely out of light. Something pulled at Shepard's mind; she knew she had seen this before.

Suddenly she was back on the Citadel. She knew it was the Citadel, although it looked nothing like the places she had been, it seemed familiar. All at once, memories flooded back to her. She had been here many times before.

"Why are you doing this? What is this?" She fumed at the child. She was not sure, but he seemed to smile.

"I am doing nothing Shepard. This is you." He spread his hands, trails of light following his movements.

Shepard yelled in frustration. Memories flooded back to her. This infuriating entity had been toying with her unendingly. She needed to break the cycle; she needed to get back to the war. This loop had to end. She looked around her for an exit, a way out, something to break the cycle. In a rage she bolted toward the child, not knowing what it would accomplish.

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><p>"Commander calm down!" A woman's voice cut through her consciousness. She felt hands holding her down. She strained against her captors; her vision was a blur of light and shadow. She could hear scuffling and beeping, but none of it made sense. "Breathe, Shepard!" Something was put in front of her face, she shook her head to fight it off. Shepard struggled harder, her breath coming in ragged gasps, her heart hammering in her chest.<p>

"For goodness sake, get her to keep still! She is going to tear her stitches!" The woman's voice was clearer this time, closer. "It's ok, Commander. It's Chakwas, lie back."

Chakwas. Shepard felt a gentle hand on her sternum; she relaxed and allowed herself to be guided back down. She tried to speak no sound came out. "Keep quiet Commander, you've been through quite an ordeal. Close your eyes, relax."

Shepard tried to steady her breathing, she closed her eyes and allowed her body to adjust. She slowly became aware of her surroundings. She could hear people murmuring around her, there were faint mechanical noises all over. She could tell her limbs felt lighter; she must not be in her armor. As she started focusing on her body, pain tore through her. Shepard was acutely aware of the blankets on her skin, of the tubing laying over her body. She felt the IV needle in her arm. With each movement, it felt as if sandpaper was scraping across her flesh. She gasped and her eyes popped open once more.

This time she could make out colors and shapes, but no detail. She saw a silver blur on a peach colored blotch.

"Commander, I am giving you another dose of morphine, the adrenaline from waking is wearing off." The peach blotch slowly came into focus as . Shepard nodded faintly and immediately regretted it. It felt as if her brain was sloshing in her skull. Her skin felt tight and her joints were stiff. She tried to relax her aching muscles. When the morphine hit her she felt a brief wash of cool before she fell into a dreamless sleep.

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><p>Dr. Chakwas walked into the makeshift waiting area outside the main London field clinic. She rubbed at her temples in a futile attempt to make her worsening headache go away.<p>

"How is she Doc?" Ashley spoke for the group assembled.

"Shepard has shown improvement. Her injuries were extensive, but she did regain consciousness today. Although her recent EKG was promising, I am still requesting the cardiologist remain at this facility in the event she takes a downturn." Chakwas smiled faintly. "However, this is the Commander we're talking about, so I expect her to make a full recovery."

Wrex grunted. "An EK-what now?"

"An electrocardiogram," Chakwas sighed. "It is a procedure human doctors use to monitor the electrical activity of the heart."

"Hmph. You better check her again Doc, she's more krogan than human, she probably has a spare heart stashed somewhere."

"Dr. Chakwas, may I see her?" Liara ventured hopefully.

"Why don't you let her rest for a few more hours, dear. Get something to eat and then we will talk about visits." Chakwas replied gently. "I need to be sure the area is sterilized before allowing visitors. Her stiches and grafts have not fully healed."

"Stiches!" Liara nearly flew out of her seat. "Why are you using such a barbaric method? We have Medi-gel for goddess sake!"

"Our supplies are critically low, Liara. The Commander already received three soldiers' worth of Medi-gel rations, and I had to fight for that. There simply aren't enough supplies to go around." Chakwas looked around at the assembled crew. Ashley had paled and was swallowing reflexively. Garrus glanced around wide eyed from Chakwas to Liara to Ashley, not comprehending the concern. Wrex simply narrowed his eyes in disgust. "We treated her most grave wounds with Medi-gel, but the ones that were less life-threatening have had to be treated the… old-fashioned way. Please, trust that I have the Commander's best interest at heart."

"Of course, I am sorry." Liara sat back, embarrassed at questioning the physician. "Please let me know when I can see her."

Chakwas nodded simply and left the Normandy crew to themselves.

"Ya see?" Wrex thumped Garrus on the back happily. "Shep's gonna be raising hell in no time! She's got quads, that one!"

Liara shook her head, but couldn't help smiling in appreciation at Wrex. Garrus coughed lightly, shooting his krogan friend a disgruntled look.

"You do realize I've only been up and about for a day right?" Garrus looked pointedly at his immobilized arm, trapped to a sling.

"Yeah, you're right. I forgot for a minute how fragile you turians are." Wrex's mouth contorted to an unseemly shape that his friends knew to be a grin. "Sorry about your wing there, comrade."

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><p>After eating a meager dinner and decontaminating herself thoroughly, Liara was allowed to see Shepard. The Commander was attached to a sizable collection of beeping and whirring machines. She slowly stepped closer, afraid to make a sound as she crossed the room.<p>

"Here," Chakwas placed a chair at Shepard's bedside. "Let me know if you need anything." She gently squeezed Liara's shoulder as she left them in peace.

"Oh Shepard," Liara ventured. She sat, tears steadily streaming down her face as she tried to keep quiet, not wanting to disturb her sleeping bondmate. She reached her hand and gently stroked Shepard's forehead with her thumb. "Goddess, I can't express what it means to see you alive."

Shepard moaned lightly, her brow furrowing. She slowly opened her eyes, focusing on the face she had wanted to see most. "Liara." Her voice was barely more than a whisper. Her face relaxed and she managed to smile slightly.

"Shhh, love, I'm here." Liara smiled in relief, delicately stroking Shepard's brown hair. She kissed Shepard's forehead and sighed happily, finally at peace for the first time in several days.


	3. Chapter 3

My my, it has been quite a while since the last chapter. I beg your forgiveness. If I told you that I was just promoted (to a big girl job!) and it is my last quarter of university, would that help? No? Shut up and get on with the story?

Your wish is my command, dear readers.

As always, thank you so much to the commenters. It means a lot to know that even a few think my story worthy of feedback. Also, thank you to everyone who has favorited, I will do my best to not lag behind anymore!

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><p>"I am warning you Commander," Chakwas addressed Shepard sternly, "if you move one inch out of that chair, I will become exceedingly unpleasant."<p>

Shepard sighed and grumbled under her breath. She did not want her first meeting with Hackett and Anderson to be conducted from a wheelchair, injuries be damned. Her progress had been remarkable thanks to the cybernetic implants Cerberus had given her.

The Commander wheeled herself out of the Normandy's medical bay, where she had been for the last four days, to the elevator and up to the conference room for her debriefing. As she moved through the scanning area, she spotted Ashley exiting the conference area.

"Skipper!" Ashley grasped Shepard's hand happily. "You're looking better and better every day. Hard to believe it's only been a week since your last surgery."

"Eight days, Ash." Shepard flashed a crooked smile in spite of her mood. "Are you headed back out for search and rescue efforts?"

"We are doing final sweeps." Ashley's grin faded. "It's been over a week since the Reapers fell; we aren't expecting many people to have survived this long out there. Most of the turians and krogan have gone back home to rebuild, but most of the quarians and geth have stayed to help find survivors across the globe."

"Really? I would think they would want to get back to Rannoch." Shepard mused.

"Well, Tali said that the quarians and geth both feel that you gave them their home world, so they want to return the favor." Williams said proudly. "The geth have been extremely useful actually, Skipper. They can scan for life signatures for greater distances and at greater depths. One Prime detected a group of nine people trapped down in the Underground yesterday."

Shepard's eyebrows shot up, "Very impressive. Good luck out there today, Ash. Let me know what I can do to help."

"Sure thing ma'am." Ashley squeezed Shepard's shoulder as she departed.

Shepard rolled into the conference room. Admirals Hackett and Anderson, along with Joker and EDI rose happily to meet her.

"It's damn good to see your face, Shepard." Anderson clapped her on the back fondly.

"I'm glad to see you're up and getting around, Commander." Hackett flashed a rare grin, "Unfortunately this isn't a social meeting. We need to debrief. The final events of the Reaper attack are unclear; I'm hoping between the five of us, we can determine exactly what happened that day. Let's start with you commander."

Shepard nodded, she had thought of little else since the invasion, but suddenly she didn't know where to begin. "Well, after the Normandy dropped us off, Liara, Garrus and I battled our way to the beacon."

Before she could continue, Hackett cut her off. "We know all of that already from their reports; we need to pick up at the point where the three of you got separated. Both Liara and Garrus said you took a direct hit from a Reaper, is that correct?"

Shepard nodded. "Yes. I remember there being a pause in ground attacks and looking up at the Reaper guarding the beam to the Citadel. It opened fire and everything went dark. I woke up and couldn't find Garrus or Liara, but I had to keep going. I took out some Marauders and got to the beam and onto the Citadel. It looked… different. Anyway, I fought my way through the wreckage to Anderson and-"

"No Shepard." Anderson interrupted gently. "I did reach the beam. I got to it with a group of four marines, but you were never there."

Shepard felt as if the wind had been knocked out of her. "But… the Catalyst, The Illusive Man…? We were with him, he… he killed himself. I had to leave you there, to continue to the Catalyst."

Anderson shook his head sadly. "I don't know what you experienced out there Shepard, but I never saw you reach the Citadel. I fought through with the marines. We had to tear through wave after wave of Cerberus troops. Eventually we reached The Illusive Man, but something happened Shepard. In the middle of our confrontation, something about him changed. He kept talking about you, like you had done something."

Shepard's eyes widened, she felt as if everything had been turned upside down. Was she crazy? "I…" She blinked fiercely and rubbed her temples, glad for once that she was in the chair, her energy had disappeared. "I don't know."

"Let's get back to what happened with you, Commander." Hackett pressed carefully. "Tell us what you remember."

Shepard looked around the table. Hackett's gaze bore into her. Anderson's face seemed guarded; he smiled slightly in an attempt to reassure the Commander. Joker sat slack-jawed, his mouth hanging open slightly. EDI gently closed his mouth, then returned her gaze to Shepard.

"Well, after I left Anderson, I reached the Catalyst. It was… damn it, I don't know what it was. It appeared to be a boy... made of light. I'm a lunatic aren't I?" Shepard's shoulders sagged, her heart raced in her chest. When no one responded she clenched her jaw and looked up. "Fine. The light-boy told me that the Reapers were created to wipe out species every 50,000 years to save them from being wiped out by their own synthetic creations."

"Uh… what?" Joker laughed in disbelief.

"Moreau." Hackett warned, glaring at him.

"Sorry Admiral, Commander." Joker sat back, biting his lip.

"Anyway," Shepard continued, ignoring Joker's outburst. "The light-boy basically told me I had three options. I could control the Reapers, merge synthetic and organic life, or destroy them. The Crucible would do any one of those three things. When he was describing the choices, I could see The Illusive Man going for the control option. I could see you, Anderson, fighting till the end for destruction of the Reapers. Then there was synthesis. It seemed so peaceful, so perfect, but I remembered Saren. That was all he wanted."

Shepard took a deep breath; the next piece of the puzzle was the difficult one. "The Catalyst told me that if I chose to destroy the Reapers, I would be destroying all synthetic life. I would destroy the geth, which would probably harm the quarians. I would be destroying you, EDI. But, I knew that Saren and The Illusive Man were wrong. The Reapers would never be controlled or coexist with organics. The only option was to destroy them. So that's what I did. I chose to destroy the Reapers by eliminating synthetic life."

The table was silent. Joker's face had gone from concern to fury. "Are you fucking kidding?" He whispered. "You chose to kill the geth, EDI?"

"Jeff, we know that's not what happened." Anderson laid a hand on Joker's shoulder.

Joker shrugged Anderson's hand off and smacked the table as hard as he dared. "I'm out of here." He rose, shaking with anger, and hobbled out of the conference room. Shepard began to wheel after him, but EDI spoke up.

"Jeff will most likely regret his reaction shortly." EDI turned to Shepard. "I do not agree with his anger. I am sure the geth would concede that your decision was the most acceptable. The destruction of the Reapers would have been the only viable solution."

"Let him go Shepard. He'll calm down." Hackett turned to Anderson. "Does any of this make sense with what The Illusive man was talking about?"

Anderson nodded, bringing himself back to the topic at hand. "One of the marines had swiped a Cerberus comm device; we could tell from their chatter that The Illusive Man was holed up in the Council Chambers. When I got to him I only had one marine with me, the others gave their lives to make sure I reached the Citadel Tower. We traded shots and he finally fell. He was defiant, raging that we were ruining his plans. But in the middle of ranting, he changed."

Anderson reached for a glass of water, pausing to gather his thoughts. "Suddenly, he was calm. I asked if he knew where he was, if he knew who he was. He told me his name was Jack, and he said there wasn't much time. He said that the Reapers had been working to indoctrinate Shepard since Sovereign came into contact with her." Anderson shifted uncomfortably, avoiding the Commander's panicked gaze.

"Cerberus had been working to help the Reapers perfect their indoctrination. They were displeased with Saren and Matriarch Benezia's relapse, and wanted to be sure Shepard could not break out of it. The Illusive Man, Jack, believed they had succeeded. The Reapers believed she was fully indoctrinated. But something happened and she broke the indoctrination anyway. He told me the Reapers were not planning on it, they had not predicted that a human could resist their best efforts. She disrupted their plans, causde an interruption in their process."

"Of course," Hackett nodded faintly, "perhaps that explains the pause."

"It seems that Shepard showed the Reapers that 1+1 can equal 3." EDI offered. When she was met with blank stares from the humans, she continued. "It is impossible to predict the behavior of organics to 100% certainty. There is a degree of chaotic behavior that, however advanced, a synthetic intelligence could never account for."

"Please explain further." Anderson watched the AI, beginning to understand what had happened.

"The Reapers, with the help of Cerberus, concluded that their indoctrination efforts would prove successful. However, Shepard broke out of the indoctrination, causing an unforeseen anomaly. The Reapers concluded that 1+1=2, but Shepard showed them that 1+1=3. They could not comprehend."

"Yes!" Anderson spoke quickly, excitedly. "The Illusive Man said she had caused a ripple through their ranks, causing their grip on his mind to loosen. That is when he told me how to activate the Catalyst and fire the Crucible."

"This meshes with what we saw during the battle." Hackett stroked his chin thoughtfully. Shepard looked at him warily. "The Reapers paused suddenly. It wasn't very long, but they just stopped moving. So I ordered the fleets to open fire. We did some heavy damage to the bastards. When they began moving again, it was as if they were disjointed. It made taking them out a hell of a lot easier than before. But there were no reports of seeing the Crucible activate."

"There wouldn't be." Anderson replied. "The Crucible is some sort of jamming signal for the Reapers. It destroyed their ability to communicate, turning their ranks from an organized hive-mind, into individuals,"

"Causing their coordinating efforts to crumble." Hackett finished. "Finally, it's all coming together."

"Yes." EDI spoke to the Admirals, but kept her gaze on Shepard. "The combination of Shepard breaking the indoctrination and the interruption of Reaper communication fits with my assessments. After engaging Reaper forces on the ground, Jeff retrieved Lieutenant Vega and Lieutenant Commander Williams and I. We then targeted what Jeff assumed to be Harbinger. Its movements were sporadic and uncalculated. After several hours, and the assistance of geth and turian ships, the Reaper fell."

"Great, so the Crucible worked, and I'm still a lunatic." Shepard spat angrily.

"On the contrary, Shepard." Hackett regarded her fondly. "You crumbled the Reaper's best efforts. You did what no one else could. If you hadn't broken through, we couldn't have taken them down."

"He's right, Shepard." Anderson smiled proudly. "You freed The Illusive Man, allowing for the activation of the Crucible."

Shepard nodded, she was suddenly exhausted. "Are we finished here?"

"I think so." Hackett stood. "Good work Shepard."

Without another word, Shepard wheeled herself out of the conference room. She ignored the greetings of crew members as she made her way to the captain's cabin rather than returning to the medical bay. She needed to be alone.


End file.
